mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| read file | reads | bases | passed filters | average | longest | mapped | |
|---|---|---|---|---|---|---|---|
| errors | 2-END_S2_L001_R1_001_150407.good.fq | 220,984 | 48,353,526 | 100.0% | 218.8 bases | 279 bases | 96.9% |
| errors | 2-END_S2_L001_R1_001_150520.good.fq | 732,080 | 167,043,246 | 100.0% | 228.2 bases | 275 bases | 98.7% |
| errors | 2-END_S2_L001_R2_001_150407.good.fq | 220,984 | 49,723,844 | 100.0% | 225.0 bases | 279 bases | 59.1% |
| errors | 2-END_S2_L001_R2_001_150520.good.fq | 732,079 | 168,533,460 | 100.0% | 230.2 bases | 275 bases | 83.2% |
| errors | GLY_02_182_S298_L001_R1_001.good.fq | 113 | 14,002 | 100.0% | 123.9 bases | 128 bases | 92.0% |
| errors | GLY_02_182_S298_L001_R2_001.good.fq | 113 | 14,002 | 100.0% | 123.9 bases | 128 bases | 69.9% |
| errors | GLY_02_182_S298_L002_R1_001.good.fq | 141 | 17,569 | 100.0% | 124.6 bases | 128 bases | 88.7% |
| errors | GLY_02_182_S298_L002_R2_001.good.fq | 141 | 17,569 | 100.0% | 124.6 bases | 128 bases | 67.4% |
| total | 1,906,635 | 433,717,218 | 100.0% | 227.5 bases | 279 bases | 87.9% |
| seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | NC_000913 | 4,641,652 | 76.1 | 3.4 | 100.0% | Escherichia coli str. K-12 substr. MG1655, complete genome. |
| total | 4,641,652 | 100.0% |
fit dispersion is the ratio of the variance to the mean for the negative binomial fit. It is =1 for Poisson and >1 for over-dispersed data.
| option | limit | actual |
|---|---|---|
| Number of alignment pairs examined for constructing junction candidates | ≤ 100000 | 1048 |
| Coverage evenness (position-hash) score of junction candidates | ≥ 2 | ≥ 2 |
| Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold | 100 ≤ n ≤ 5000 | 92 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.011 |
| reference sequence | pr(no read start) |
|---|---|
| NC_000913 | 0.87785 |
pr(no read start) is the probability that there will not be an aligned read whose first base matches a given position on a given strand.
| option | value |
|---|---|
| Coverage evenness (position-hash) score of predicted junctions must be | ≥ 3 |
| Skew score of predicted junction (−log10 probability of unusual coverage evenness) must be | ≤ 0 |
| Number of bases that at least one read must overlap each uniquely aligned side of a predicted junction | ≥ 6 |
| option | value |
|---|---|
| Mode | Full Polymorphism |
| Ploidy | 1 (haploid) |
| Consensus mutation E-value cutoff | 10 |
| Consensus frequency cutoff | 0.75 |
| Consensus minimum variant coverage each strand | OFF |
| Consensus minimum total coverage each strand | OFF |
| Consensus minimum variant coverage | OFF |
| Consensus minimum total coverage | OFF |
| Polymorphism E-value cutoff | 2 |
| Polymorphism frequency cutoff | 0.05 |
| Polymorphism minimum variant coverage each strand | 2 |
| Polymorphism minimum total coverage each strand | OFF |
| Polymorphism minimum variant coverage | OFF |
| Polymorphism minimum total coverage | OFF |
| Polymorphism bias cutoff | OFF |
| Predict indel polymorphisms | YES |
| Skip indel polymorphisms in homopolymers runs of | ≥3 bases |
| Skip base substitutions when they create a homopolymer flanked on each side by | ≥5 bases |
| program | version |
|---|---|
| bowtie2 | 2.3.4.1 |
| R | 3.4.4 |
| step | start | end | elapsed |
|---|---|---|---|
| Read and reference sequence file input | 16:08:31 02 Jan 2019 | 16:09:06 02 Jan 2019 | 35 seconds |
| Read alignment to reference genome | 16:09:06 02 Jan 2019 | 16:18:49 02 Jan 2019 | 9 minutes 43 seconds |
| Preprocessing alignments for candidate junction identification | 16:18:49 02 Jan 2019 | 16:19:16 02 Jan 2019 | 27 seconds |
| Preliminary analysis of coverage distribution | 16:19:16 02 Jan 2019 | 16:20:51 02 Jan 2019 | 1 minute 35 seconds |
| Identifying junction candidates | 16:20:51 02 Jan 2019 | 16:20:52 02 Jan 2019 | 1 second |
| Re-alignment to junction candidates | 16:20:52 02 Jan 2019 | 16:22:43 02 Jan 2019 | 1 minute 51 seconds |
| Resolving best read alignments | 16:22:43 02 Jan 2019 | 16:23:33 02 Jan 2019 | 50 seconds |
| Creating BAM files | 16:23:33 02 Jan 2019 | 16:24:52 02 Jan 2019 | 1 minute 19 seconds |
| Tabulating error counts | 16:24:52 02 Jan 2019 | 16:25:26 02 Jan 2019 | 34 seconds |
| Re-calibrating base error rates | 16:25:26 02 Jan 2019 | 16:25:28 02 Jan 2019 | 2 seconds |
| Examining read alignment evidence | 16:25:28 02 Jan 2019 | 17:02:56 02 Jan 2019 | 37 minutes 28 seconds |
| Polymorphism statistics | 17:02:56 02 Jan 2019 | 17:02:56 02 Jan 2019 | 0 seconds |
| Output | 17:02:56 02 Jan 2019 | 17:03:07 02 Jan 2019 | 11 seconds |
| Total | 54 minutes 36 seconds | ||
